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Papuan forests have been subjected to shifting cultivation for centuries by indigenous people affecting the ecological processes therein; during secondary succession, fallow forests recover naturally. However, the information on ecological succession after swidden practices remains poorly understood in Papuan lowland forests. This study aimed to examine the plant species richness and density of different plant lifeforms in fallows of increasing time after slash-and-burn cultivation along with basic edaphic factors. We performed data collection in the northern part of the lowland evergreen tropical forest near Manokwari, West Papua, Indonesia. The sampling consisted of 26 plots distributed in the primary forest (n = 6) and in secondary/fallow forests 2-, 4-, 7-, and 9-years after cultivation (n = 5 for each age class). The plant community in primary forest clearly differed from the secondary forests. The plant species richness was about twice as high in primary compared to secondary forests. The density of trees and shrubs increased during succession whereas that of lianas declined. The soil fertility declined in secondary forests, although soil organic matter was greatest two years after swidden and then decreased gradually over time. This research underlined that indigenous swidden practices alter ecological conditions and that secondary forests will take a long time to fully recover to resemble primary forest. Hence, the monitoring of vegetation during the process is necessary to inform conservation programs.